The PURE course, which promotes the traditional marriage as the best setting for a sexual relationship, was banned following protests from other students, particularly members of the Gay and Lesbian Society at the university.
Claims that promotional material for the six-week course included stories from people who had been "cured" of their homosexuality, university chiefs defended its decision to ban the course on the grounds that it broke equality and diversity rules.
Spokesman for the Catholic Church in Scotland Peter Kearney said: "This is nothing more than blind and unthinking political correctness."
The Lawyers' Christian Fellowship also criticised the decision to ban PURE, saying, "This incident is an attack on freedom of speech in an institution where an open exchange of views and a search after truth should be strongly upheld.
"In this instance the Christian Union is being denied freedom of expression because what they say and believe is uncomfortable for some groups in the university."
Laura Stirrat, vice-president of Edinburgh University's Christian Union, said: "The university is effectively closing down free speech."
Churches across the country are also offering their prayerful support for the Christian Unions. Deal Christian Fellowship in Kent is just one of many churches urging members to write to the principal of Edinburgh University expressing their disapproval of the censure.
Edinburgh University remains unapologetic. A university spokeswoman said the course was "contradictory to our equality and diversity values" and that it was not appropriate to run on university or Students Association premises.
Now Edinburgh University Christian Union is among several Christian Unions across the country seeking legal advice after they were also banned by their university authorities or had their privileges withheld.
The 150-strong Christian Union in Birmingham was suspended this year after refusing to alter its constitution to allow non-Christians to address meetings and to amend its literature to include references to gays, lesbians, bisexuals and those of transgender sexuality.
Christian students are threatening to take Exeter University and students' guild to court over human rights breaches after the university temporarily suspended the Christian Union from the official list of student societies on campus.
Exeter Christian Union told the university last Thursday that it would take legal action after 14 days if it was not fully re-instated as a student society by the guild with full rights and was allowed to call itself the Christian Union.